Open wgmao opened 3 years ago
@wgmao
Hi. Thank you for your interest in CookHLA.
(1)
Before investigating, did you create and apply a new virtual conda environment for CookHLA with the given YML file? ('CookHLA_[YOUR_OS].yml')
If you did the above, then there would be an PLINK error log file('MyAGM/1958BC.hg19.COPY.LiftDown_hg18.log', supposedly.) Can you share it? It seems PLINK failed to generate 'MyAGM/1958BC.hg19.COPY.LiftDown_hg18.{bed,bim,fam}' files in this code block(https://github.com/WansonChoi/CookHLA/blob/56df6e2d5f656179f4be5fb73e443b7e2804bfc3/src/checkInput.py#L210)
(2) The reference panels for each population were divided from one panel with all samples(n=2504). I pushed them in the '1000G_REF/' directory. (1000G_REF.ALL.chr6.hg18.29mb-34mb.inT1DGC.{bed,bim,fam, ...}).
Thank you very much for your help.
1) I didn't create a new virtual environment, but I put all external software in the dependency
folder and installed the requirements. Is it necessay to create the environment with the given YML file? I just found that the list of dependency software is much longer than that listed in the README.md
. Maybe I miss a lot of the dependency package for R and python.
2) I have found these files and they are really helpful.
@wgmao
To control other unexpected variables, It is recommended to create and use a new conda environment, but I think the dependency is not highly related to this error. So, let's suspect other things first.
I guess the error is more related to the preprocesses that the 'src/checkInput.py' performs. I recently modified it, so apply this update(the commit 'c873550') and try the 'MakeGeneticMap' module again, please. If it fails with a similar error, then please share the log file(maybe '*.COPY.LiftDown_hg18.log').
Thank you for developing this wonderful tool. I have two questions for you as I failed to reproduce the toy example.
When I tried to generate the adaptive genetic map using the toy dataset available in the folder, I got the following errors. I have created
MyAGM
folder in the working directory, so I don't know if I missed anything.Is there a way to merge reference panels, e.g., all 1000Genome panels?